<link rel="shortcut icon" href="
{$system['system_url']}/themes/{$system['theme']}/images/favicon.png" />
This line is used to set favicon but they can use direct the image url "images/favicon.png" so why they used

The theme publisher is making it so that the template need not be changed for each sub-theme that could exist, and for installations that may exist in a sub-folder.

There should be a theme descriptor file where the sub-themes can be defined. Then, {$system['theme']} could be:
my_theme/steel_blue
and {$system['system_url']} could be:
www.mysite.com/wholesale_store
This allows for arbitrary flexibility where otherwise, one would need to specifically find the relevant statements and re-code all templates in a theme.